Archive for category Publishing

Interview on national newspaper regarding the publish or perish atmosphere

I was interviewed, along with other fellow Chilean scientists, for a piece (in Spanish) on the publish-or-perish culture, the tyranny of the Impact Factor and the pressure on scientists to publish in top journals for career advancement, among other things. The article, written by Tania Opazo and entitled “The Tyranny of Scientific Publications”, appeared today in “La Tercera”.

Go check it out!

Dibujo

Cover of the issue including the article. The title reads “My life for a paper”

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Embracing minimal guidelines for the reporting of RT-qPCR experiments: responsibility lies on both ends

In mid-2012, Stephen A. Bustin, Jo Vandesompele and myself, decided to send a letter to the editor of a glam magazine asking for journals to demand authors to provide at least minimal information for the critical evaluation and reproducibility of published RT-qPCR experiments. The lack of information regarding these experiments is inversely proportional to the IF of the journal: the higher the IF, the lower the amount of information provided for these experiments (See Nat Methods. 2013 Nov;10(11):1063-7). It was no surprise then, considering that they were the ones we targeted in the letter (although not explicitly), that glam journals (you know which…) refused publishing the letter.

I found the letter searching for something else in my computer and decided to share it with you, just as it was written back in 2012. The main theme is as true as it was back then.

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Correspondence

Alejandro Montenegro-Monteroa
Stephen A. Bustinb
Jo Vandesompele c

a Department of Molecular Genetics and Microbiology, Faculty of Biological Sciences, Pontificia Universidad Católica de Chile.
Email: aemonten@uc.cl. Tel: (+562) 6862348
b Queen Mary University of London, UK
Email: stephen.bustin@qmul.ac.uk. Tel: (+44) 2073777000
c Center for Medical Genetics, Ghent University, Belgium
d Biogazelle, Zwijnaarde, Belgium.
Email: Joke.Vandesompele@UGent.be. Tel: (+32) 479353563.

To the Editor:

Reverse transcription real-time quantitative PCR (RT-qPCR) is currently the most widely used molecular method for the detection and quantification of RNA. RNA integrity and purity, primer sequences and their specificity, assay efficiency and identification of appropriate reference genes are just a few of the essential parameters that must be assessed and reported when using this quantitative technique. Most authors however, fail to include them, either in the methods or the online supplementary sections, with some arguably not even having performed the appropriate controls. As has been previously reported, this can lead to flawed data and wasted efforts in trying to reproduce results that can be, in some cases, artifacts and thus not biologically relevant1.

The MIQE guidelines2,3 were proposed to enhance experimental accuracy and transparency and to enable the research community to assess reported data and reproduce published qPCR experiments. The guidelines should be considered a complete “checklist” to be used as a reference for the reporting of results. While the response to these guidelines has been largely positive, in both commercial and research settings, most currently published articles that include qPCR experiments fail to properly report experimental procedures.

Although it is the authors’ task to embrace minimal guidelines that allow for reproducibility and transparency of their studies, journal editors have a responsibility to demand such information. Even though some publishers have implemented the MIQE guidelines or at least the bulk of the recommendations, many top-tier journals continue to publish research that grossly lacks the required information not only to reproduce the reported experiments, but also to evaluate properly the conclusions derived from them. Given that the number of retractions is on the increase, that the majority of retractions are caused by poor experimental protocols and that once published in the peer-reviewed literature, even a rebuttal does not affect a paper’s frequency of citation, we would like to issue a wakeup call to journal editors and publishers.

We urge journals to demand that all manuscripts include such minimum information, in the form of the MIQE or other guidelines, to ensure the accuracy and reproducibility of the reported results. The use of online supplementary sections makes the often used “space constraint” argument no longer valid.

1. Lanoix, D. et al. Quantitative PCR Pitfalls: The Case of the Human Placenta. Mol Biotechnol (2012).
2. Bustin, S.A. et al. The MIQE guidelines: minimum information for publication of quantitative real-time PCR experiments. Clin Chem 55, 611-622 (2009).
3. Bustin, S.A. et al. Primer sequence disclosure: a clarification of the MIQE guidelines. Clin Chem 57, 919-921 (2011).

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Abstract word cloud from glam journals – 2013 edition.

Quick and simple post, considering it is Jan 1st and I’m still tired from last night, and the fact that I just came back from, you guessed it, the lab.

Anyway, I wanted to know what the most recurring topics were on the top two glam journals during 2013, so I obtained the 2013 PubMed-indexed abstracts from Nature and Science using EBOT and then used Wordle to generate a word cloud.

Here are the results:

1) Nature

Image2) Science

ImageCool, ah? You’ll notice that many words are shared.

It’s pretty easy to do it for any other journal or for any other query in PubMed using Ebot. If you want to do something similar for say, your country or institution and you need help, let me know.

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Quotes from the science blogosphere: Comparing the content of glam journals & specialized ones

Percentage-wise, there is less bullshit in specialized journals. But there is still a lot of it there. Notably, the percent of bullshit that draws attention and is dealt with in decisive fashion is definitely higher in glamour mags.

-DK, as a comment to a post discussing peer review.

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Quotes from the science blogosphere

An IF of 4.4 for a journal less than 5 years old, that does not pump up its IF by publishing review articles, and that does not pre-screen for scientific impact, is nothing less than remarkable

-Alex Merz (referring to PLoS ONE), in a comment at the Scholarly Kitchen

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About the RWA parody at The Scholarly Kitchen

Interested in scholarly publishing? If you are reading this blog, I’m sure you are (I’m assuming you are a scientist. If you are not, let me know! I’d love to know who else is reading this).

Please take a look at this post by Kent Anderson (CEO/Publisher of the Journal of Bone & Joint Surgery, Inc), entitled “Revisiting a Little-Known RWA of the Past — The Restaurant Welfare Act of 1958“, a “satire” wrote about the Research Works Act. This is at the Scholarly Kitchen blog.

I won’t comment about it here; instead, I strongly advise you to read it, particularly the comments section, in which Anderson takes a swing at the PLoS ONE business model when Michael Eisen starts commenting.
Some of Anderson’s arguments, in which he clearly exhibits his disdain for PLoS One, appeal to a somewhat outdated publishing “world”, in which the internet and its ability to connect scientists from all over the world and find new research articles, regardless of where they are published, is not considered.

He claims that journals serve only two purposes, “quality validation and relevance signaling” and that PLoS ONE does neither. My comment above goes to the 2nd statement. I don’t need a journal to tell me what articles to read. Library days are over. I won’t go the library and pick up a copy of Nature or PNAS (or whatever journal has published an article related to my work, at least once) and hope there’s something there related to my research. I have email alerts now and have all the information, from all journals (currently I’m getting my alerts from Pubmed), so I can find articles related to my research. Hopefully, when I click on the links I get, I’ll be able to download the article in order to evaluate it…

(and before you say anything, no… I don’t think that just by looking at the journals indexed in Pubmed, I’m supporting the ‘relevance signaling’ argument. Do you know how many journals are in there? And PLoS ONE is there too).

This is how Mike Taylor puts it:

As a point of information, the relevance signalling part of this is no longer true (though it used to be). It’s now been many years since I read a paper on the basis of what journal it was published in rather than what it contains. Most papers I read, I am hardly even aware of what journal it’s in.

To which Anderson replies “well, that’s your experience“.

Anyway…. take a look at the parody.

 

Update (14Feb2012). Anderson blocked the comments on his post.

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